Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
Browse
2 results
Search Results
Now showing 1 - 2 of 2
Master Thesis Peptide Hydrogels Containing Cell Attachment Molecules(Izmir Institute of Technology, 2019) Uysal, Berk; Top, Ayben; Top, AybenIn this study, peptides with sequences and notations as KLELKLELKLEL (KLEL), KLDVKLDVKLDV (KLDV), KLDVKLDVKLKV (KLKV1), KLKVKLDVKLKV (KLKV2), KLKVKLKVKLKV (KLKV3) were synthesized using solid phase peptide synthesis (SPPS) method based on Fmoc chemistry. Reverse phase HPLC and MALDI-TOF mass spectroscopy characterization methods were used to assess the purity of the peptides. Three different synthesis procedures were tested, and it was found that employing DMF:DMSO at 1:1 ratio as a solvent increased purity of the resultant peptide. FTIR results indicated the presence of expected β-sheet secondary structure, as well as an interference band from TFA salts for all of the peptides. All the peptides formed hydrogels at pH 7.4 with 1 wt% concentration in deionized water (DIW). AFM results of these hydrogels indicated that KLKV1 and KLKV2 had fibrous morphology with a width of 5-20 nm and 7-18 nm respectively. KLDV and KLKV3 peptide hydrogels, on the other hand, exhibited globular structures, having sizes with 15-50 nm and 8-15 nm, respectively. Storage moduli (G’) of these hydrogels in DIW were obtained as ~860 ± 150 Pa, ~260 ± 60 Pa, ~210 ± 30 Pa and ~1850 ± 200 Pa for KLDV, KLKV1, KLKV2 and KLKV3 respectively. Of these peptides, only HCl salt of KLDV and KLKV1 peptides more readily formed hydrogels in PBS but at 1.5 wt% concentration. G’ values of these KLDV and KLKV1 hydrogels were determined as ~1810 ± 850 Pa and ~700 ± 230 Pa, respectively. Cell proliferation tests (CCK-8 assay) of KLDV and KLKV1 hydrogels were performed by using L929 mouse fibroblast cells. Empty wells (TCPS) were used as a control group. Cell proliferation was observed to be comparable for both select hydrogels and empty wells, suggesting possible applications of these hydrogels in tissue engineering.Master Thesis Exploiting Fragment-Ion Complementarity for Peptide De Novo Sequencing From Collision Induced Dissociation Tandem Mass Spectra(Izmir Institute of Technology, 2011) Aytun, Belgin; Allmer, JensPeptide identification from mass spectrometric data is a key step in proteomics because this field provides sequence, quantitative, and modification data of actually expressed proteins. Two approaches are generally deployed to interpret experimental MS/MS data, database searching and de novo sequencing. Database search method has been used successfully in proteomics projects for organisms with well-studied genomes. However, it is not applicable in situations where a target sequence is not in the protein database. This can happen for a number of reasons, including novel proteins, protein mutations and post-translational modifications. Because of the disadvantages of database searching method, a lot of research has focused on de novo sequencing method which assigns amino acid sequences to MS/MS spectra without the need for a database. The aim of this study is to enhance the accuracy of de novo sequencing tools. One step commonly employed in all de novo sequencing tools is naming of fragment ions. It is essential to know which peak represents which ion type in order to traverse a spectrum graph to find an amino acid sequence that best explains the MS/MS spectrum. Different approaches have been tried to name ions and some success has been achieved in naming b-type ions and y-type ions. We have presented a new approach which enables the naming of not only b- and y-type ions but other arbitrary ion types as well. This enabled the detection of b-ion ladder. In the latter case, missing fragments were determined by using other named ion types. Furthermore, unexplained data in tandem mass spectra were reduced as much as possible. Therefore, a complete sequence will be derived by the new approach.